WIP: Specification of Timecourses #581
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* extract all changes from previous * fixup * allow hyphens in extension names * fixup hyphens * only require one toolbox that implements extension * specify how to work with multiple PEtab problems * specify we do not require a quorum number of votes * allow test cases to be provided by the extension library * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>
PEtab extensions were introduced in #537. We should be able to distinguish there between optional extensions and required extensions, i.e. those that modify the parameter estimation problem as such, and those that just add additional/optional information (e.g. annotations, info for visualization, ...). If some tool does not know about a certain optional extension, it can safely be ignored during import, if it does not know about a required extension, it should fail. This PR adds a `required` attribute to extensions in the yaml file to indicate whether they are required for the mathematical interpretation of the PEtab problem. Resolves #544
Co-authored-by: Dilan Pathirana <[email protected]>
- remove preequilibrationConditionId - remove simulationConditionId - add timecourseID
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May 30, 2024
Previously, the math expression syntax wasn't specified. This was very problematic, because different libraries and programming languages have different names for the same functions, and more importantly, differ in operator precedence. Co-authored-by: Dilan Pathirana <[email protected]> Co-authored-by: dilpath <[email protected]>
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Resolved merge conflicts. This needs to be updated to match the new mostly-agreed-upon format in #586
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Add basic support for PEtab version 2 experiments (see also PEtab-dev/PEtab#586, and PEtab-dev/PEtab#581). Follow-up to #334. Partially supersedes #263, which was started before petab.v1/petab.v2 were introduced and before PEtab-dev/PEtab#586. * updates the required fields in the measurement table * updates some validation functions to not expect the old `simulationConditionId`s (but does not do full validation yet) * extends PEtab v1 up-conversion to create a new experiment table. --------- Co-authored-by: Dilan Pathirana <[email protected]>
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FFroehlich
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Feb 5, 2025
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| We distinguish between three types of entities: | ||
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| * Entities that are defined in terms of a time-derivative, e.g., the targets |
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| * Entities that are defined in terms of a time-derivative, e.g., the targets | |
| * **Differential Targets**: Entities that are defined in terms of a time-derivative, e.g., the targets |
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| * Entities that are defined in terms of a time-derivative, e.g., the targets | ||
| of SBML rate rules or non-constant species participating in reactions. | ||
| Referred to as `differential targets` below. |
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| Referred to as `differential targets` below. |
| +--------------+------------------+------------------+-----------------+--------------------+ | ||
| | conditionId1 | conditionName1 | modelEntityId1 | setCurrentValue | 0.42 | | ||
| +--------------+------------------+------------------+-----------------+--------------------+ | ||
| | conditionId1 | conditionName1 | modelEntityId2 | | 0.42 | |
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according to below, operationType is required
| +--------------+------------------+------------------+-----------------+--------------------+ | ||
| | conditionId1 | conditionName1 | modelEntityId2 | | 0.42 | | ||
| +--------------+------------------+------------------+-----------------+--------------------+ | ||
| | conditionId2 | ... | modelEntityId1 | | modelEntityId1 + 3 | |
| values as defined in the model). | ||
| The target must be a constant target or a differential target. | ||
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| - ``setRate``: The time-derivative of the target is set to ``targetValue`` |
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It seems natural to have an addToCurrentValue as well
| in the model. ``-inf`` indicates pre-equilibration (e.g., for drug | ||
| treatments, the model would be pre-equilibrated with the no-drug condition). | ||
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| - ``CONDITION_ID``: Reference to a condition ID in the condition table that |
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[PETAB_ID, REQUIRED, REFERENCES(conditions.conditionID)]
| @@ -519,7 +699,7 @@ Additional columns may be added. | |||
| Detailed field description | |||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~ | |||
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| - ``parameterId`` [STRING, NOT NULL] | |||
| - ``parameterId`` [STRING, REQUIRED] | |||
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| - ``parameterId`` [STRING, REQUIRED] | |
| - ``parameterId`` [PARAMETER_ID, REQUIRED] |
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| - ``experimentId`` [STRING, REQUIRED] | ||
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| Identifier of the experiment. The usual PEtab identifier requirements apply. |
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| Identifier of the experiment. The usual PEtab identifier requirements apply. | |
| Identifier of the experiment. |
| This is specified as a tab-separated value file in the following way: | ||
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| +---------------------+-------------------+-----------------+ | ||
| | experimentId | time | conditionId | |
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While I agree that we can drop the name in the conditions table, I think it would be nice to have an optional name column here.
| @@ -757,14 +939,14 @@ The TSV file has two mandatory columns, ``petabEntityId`` and | |||
| Detailed field description | |||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~ | |||
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| - ``petabEntityId`` [STRING, NOT NULL] | |||
| - ``petabEntityId`` [STRING, REQUIRED] | |||
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| - ``petabEntityId`` [STRING, REQUIRED] | |
| - ``petabEntityId`` [PETAB_ID, REQUIRED] |
dilpath
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Feb 6, 2025
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| - A model | ||
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| - A measurement file to fit the model to [TSV] | ||
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| - A condition file specifying model inputs and condition-specific parameters | ||
| - (optional) A condition file specifying model inputs and condition-specific parameters |
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I think we usually refer to this as the "conditions table"
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| - (optional) A condition file specifying model inputs and condition-specific parameters | |
| - (optional) A conditions file specifying model inputs and condition-specific parameters |
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| - ``NON_ESTIMATED_ENTITY_ID``: A string that is a valid PEtab ID and refers | ||
| to an entity that has some associated numeric value and is not estimated, | ||
| e.g., a model parameter, parameter table parameter, or a species in the | ||
| model. |
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| - ``NON_ESTIMATED_ENTITY_ID``: A string that is a valid PEtab ID and refers | |
| to an entity that has some associated numeric value and is not estimated, | |
| e.g., a model parameter, parameter table parameter, or a species in the | |
| model. | |
| - ``NON_ESTIMATED_ENTITY_ID``: A string that is a valid PEtab ID and refers | |
| to an entity that has some associated numeric value (e.g. a model parameter, | |
| parameter table parameter, or a species in the model) and is not estimated. |
| * Clarification and specification of various previously underspecified aspects | ||
| (math expressions, overriding values in the condition table, etc.) | ||
| (:ref:`math_expressions`, overriding values in the condition table, etc.) |
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Should list everything (explicitly or by some grouping)
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| (:ref:`math_expressions`, overriding values in the condition table, etc.) | |
| (:ref:`math_expressions`, overriding values in the condition table) |
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| The conditions table specifies changes to parameters, initial values of species | ||
| and compartments for specific simulation conditions. Different conditions can | ||
| be combined to form time courses or experiment through the | ||
| :ref:`experiments_table`. Any changes applied to the model will remain in | ||
| effect until they are changed by a subsequent condition. |
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| The conditions table specifies changes to parameters, initial values of species | |
| and compartments for specific simulation conditions. Different conditions can | |
| be combined to form time courses or experiment through the | |
| :ref:`experiments_table`. Any changes applied to the model will remain in | |
| effect until they are changed by a subsequent condition. | |
| The conditions table specifies changes to parameters, initial or intermediate values of | |
| species, and compartments, during specific time periods. The start and end of the time | |
| period is defined in the :ref:`experiments_table`, where multiple conditions can be | |
| combined to specify time courses or experiments that span multiple time periods. Any | |
| changes applied to the model will remain in effect until they are changed by a condition | |
| applied at a later time period. |
| | ... | ... | ... | | ... | | ||
| +--------------+------------------+------------------+-----------------+--------------------+ | ||
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| Each line specifies a change of one specific property of a specific entity. |
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| Each line specifies a change of one specific property of a specific entity. | |
| Each line specifies the change in the numeric value of one specific non-estimated entity. |
| We distinguish between three types of entities: | ||
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| * Entities that are defined in terms of a time-derivative, e.g., the targets | ||
| of SBML rate rules or non-constant species participating in reactions. |
There was a problem hiding this comment.
Suggested change
| of SBML rate rules or non-constant species participating in reactions. | |
| of SBML rate rules or species that change by participating in reactions (educts or products). |
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| For any conditionId with ``operationType=noChange``, there must not be any | ||
| other row with the same ``conditionId`` in the conditions table. |
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Suggested change
| For any conditionId with ``operationType=noChange``, there must not be any | |
| other row with the same ``conditionId`` in the conditions table. | |
| For any ``conditionId`` with ``operationType=noChange``, there must not be any | |
| other row with the same ``conditionId`` in the conditions table. |
| +---------------------+-------------------+-----------------+ | ||
| | experimentId | time | conditionId | | ||
| +=====================+===================+=================+ | ||
| | PETAB_ID | NUMERIC or '-inf' | CONDITION_ID | |
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Agreed, in the measurements table it is NUMERIC\|inf instead
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| Note: The time interval in which a condition is applied includes the | ||
| respective starting timepoint, but excludes the starting timepoint of | ||
| the following condition. This means that for an experiment | ||
| ``[time_A:condition_A; time_B:condition_B]``, ``condition_A`` is active | ||
| during the interval ``[time_A, time_B)``. This implies that any event | ||
| assignment that triggers at ``time_B`` will occur *after* ``condition_B`` was | ||
| applied and for any measurements at ``time_B``, the observables will be | ||
| evaluated *after* ``condition_B`` was applied. |
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This is the old (not long format) version of the experiments table, so it might be confusing to users
Suggested change
| Note: The time interval in which a condition is applied includes the | |
| respective starting timepoint, but excludes the starting timepoint of | |
| the following condition. This means that for an experiment | |
| ``[time_A:condition_A; time_B:condition_B]``, ``condition_A`` is active | |
| during the interval ``[time_A, time_B)``. This implies that any event | |
| assignment that triggers at ``time_B`` will occur *after* ``condition_B`` was | |
| applied and for any measurements at ``time_B``, the observables will be | |
| evaluated *after* ``condition_B`` was applied. | |
| Note: The time interval in which a condition is applied includes the | |
| respective starting timepoint, but excludes the starting timepoint of | |
| the following condition. This means that for an experiment where | |
| ``condition_A`` is applied at ``time_A`` and later ``condition_B`` is | |
| applied at ``time_B``, then ``condition_A`` is active | |
| during the interval ``[time_A, time_B)``. This implies that any event | |
| assignment that triggers at ``time_B`` will occur *after* ``condition_B`` was | |
| applied and for any measurements at ``time_B``, the observables will be | |
| evaluated *after* ``condition_B`` was applied. |
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| Multiple conditions can be applied at the same time point by specifying | ||
| multiple lines with the same ``experimentId`` and ``time`` but different | ||
| ``conditionId``. The order of the conditions is arbitrary **????**. | ||
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| **TODO** how to deal with conflicts? |
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Suggestion based on previous conversations, not sure how to word it best though
Suggested change
| Multiple conditions can be applied at the same time point by specifying | |
| multiple lines with the same ``experimentId`` and ``time`` but different | |
| ``conditionId``. The order of the conditions is arbitrary **????**. | |
| **TODO** how to deal with conflicts? | |
| Multiple conditions can be applied at the same time point by specifying | |
| multiple lines with the same ``experimentId`` and ``time`` but different | |
| ``conditionId``. The order of the conditions is arbitrary. | |
| All changes across all simultaneous conditions are applied in order of | |
| dependencies, with conservation of mass when volumes change, i.e. | |
| a volume change implies a concentration change, but not vice versa. | |
| Hence, volume changes are applied before concentration changes in the | |
| same compartment, and changes to parameters are applied before | |
| changes to species that depend on the parameters. |
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This draft PR adds the descriptions from the Time course specification to the
release/2.0.0branch.preview site is: https://petab--581.org.readthedocs.build/en/581/documentation_data_format.html#timecourses-table